Software Taxonomy Biology

Software Taxonomy Biology

Top: Science: Biology: Taxonomy: Software

Editor's Picks:

- PAUP is the most widely used package for phylogenetic inference, and now implements maximum likelihood and distance methods as well as various forms of parsimony. Powerful and very easy to use, particularly the Mac version.
PHYLIP

- Joe Felsenstein's suite of programs implementing perhaps the widest range of phylogenetic inference package. The most widely distributed phylogeny software. Includes distance, likelihood and parsimony methods for a wide range of different types of data, a

SuperTree - Implements various supertree building methods. Available in Linux/Unix and PC versions.
Component - For analysis of phylogenies. Includes a wide range of randomization methods, consensus methods, tree comparison measures, and calculates reconciled trees. Now aging, and available only for Windows machines, but still has some unique features. Much of the
GeneTree - Uses reconciled trees to compare gene trees and species trees, explaining incongruence between the phylogenies by postulating horizontal transfer, gene duplication and loss events. Reprints of papers describing the methods are available from the GeneTree
r8s - Open source software for estimating absolute rates of molecular evolution and divergence times on phylogenetic trees.
TreeMap - Experimental program for comparing host and parasite trees.
Phylo-Win - Graphical color interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony, and maximum likelihood methods and bootstrap with any of them.
Clann: Software for Supertree Methods - Clann implements a large number of supertree methods for reconstructing phylogenies from sets of input phylogenetic trees.
PAML - Phylogenetic analyses of DNA or protein sequences using maximum likelihood.
MacClade - A powerful Macintosh package for phylogenetic analysis. Not intended as a stand-alone tool to infer phylogeny, but excels in studying character evolution. Also provides tools for entering and editing data and phylogenies and producing attractive tree diag
MrBayes - Open source software for estimation of phylogenies using Bayesian inference.
Tree Puzzle - Computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.
NONA - A Quick Guide to the Commands - A brief overview of using NONA for phylogenetic analysis.
TreeView - Simple program for displaying phylogenies.
NONA - Freeware software for phylogenetic analyses using parsimony.
3I - Internet-accessible Interactive Identification - Program to create internet-accessible interactive taxonomic keys.
Mesquite - Experimental, modular software for evolutionary biology, designed to help biologists analyze comparative data about organisms.
Phylodendron - Java application for drawing phylogenetic trees. Allows you to save in various formats, print, edit, modify, and adorn the tree, and should work on any java runtime platform.

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